Related papers: Mesoscopic model for nano-channel confined DNA
Quantum confinement of the perpendicular motion of electrons in single-crystalline metallic superconducting nanofilms splits the conduction band into a series of single-electron subbands. A distinctive feature of such a nanoscale multi-band…
We report on a molecular simulation method which captures the self-assembly of cationic lipid-DNA (CL-DNA) gene delivery complexes. Computational efficiency required for large length- and time-scale simulations is achieved through a…
We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account…
We study the random walk of a particle in a compartmentalized environment, as realized in biological samples or solid state compounds. Each compartment is characterized by its length $L$ and the boundaries transmittance $T$. We identify two…
The effect of a finite torque on semiflexible polymers in a confined environment is investigated. It is shown how a new lengthscale appears in the strongly confined limit. The influence of a torque on the extension of biopolymers in…
The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the…
Using molecular dynamics simulation, we investigate transport properties of a classical two-dimensional electron system confined in a microchannel with a narrow constriction. As a function of the confinement strength of the constriction,…
We consider the lattice model for an ideal-linear polymer chain to mimic the conformations of the semi-flexible homo-polymer chain. The polymer chain is assumed to confine in the fairly small area, such that the flexible chain conformations…
Simulating percolation and critical phenomena of labelled species inside films composed of single-component linear homogeneous macromolecules using molecular Monte Carlo method in 3 dimensions, we study dependence of these conducting…
This paper considers particle propagation in a cylindrical molecular communication channel, e.g. a simplified model of a blood vessel. Emitted particles are influenced by diffusion, flow, and a vertical force induced e.g. by gravity or…
While analyzing the persistence length of DNA atomistic simulations Wu et al. [J. Chem. Phys. 142, 125103 (2015)] introduced an empirical formula to account for the observed length-dependence. In particular they found that the persistence…
Relying on symmetry considerations appropriate for helical biopolymers such as DNA and filamentous actin, we argue that crystalline packings of mutually repulsive helical macromolecules fall principally into two categories: unfrustrated…
The motion of quantum particles homogeneously constrained to a curved surface is affected by a curvature induced geometric potential. Here, we consider the case of inhomogeneous confinement and derive the effective Hamiltonian by extending…
We report a molecular dynamics simulation of a supercooled simple monatomic glass-forming liquid. It is found that the onset of the supercooled regime results in formation of distinct domains of slow diffusion which are confined to the…
We have studied the extended Hubbard model with pair hopping in the atomic limit for arbitrary electron density and chemical potential. The Hamiltonian considered consists of (i) the effective on-site interaction U and (ii) the intersite…
Particle suspensions in confined geometries can become clogged, which can have a catastrophic effect on function in biological and industrial systems. Here, we investigate the macroscopic dynamics of suspensions in constricted geometries.…
When it is viewed at the scale of a base pair, DNA appears as a nonlinear lattice. Modelling its properties is a fascinating goal. The detailed experiments that can be performed on this system impose constraints on the models and can be…
The ubiquitous biomacromolecule DNA has an axial rigidity persistence length of ~50 nm, driven by its elegant double helical structure. While double and multiple helix structures appear widely in nature, only rarely are these found in…
We study a ferromagnetic suspension or a suspension of magnetic nanoparticles in an anisotropic nematic medium, in three different one-dimensional variational settings, ordered in terms of increasing complexity. The three models are…
Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure…